Life's Ratchet: How Molecular Machines Extract Order from Chaos
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Regression toward the mean, 55–56
Regulation, 231–233, 235–237
Regulatory networks, 235–237
Renaissance, 18
Rennin, 112
Repair enzymes, 64, 117
Replication, 202–205
Repressor protein, 236
Reset step
ATP hydrolysis in myosin V and, 186–187
in kinesin-1, 181
for molecular machines, 155–158
Reversibility, 133–136
Reversible machine, 158
Ribosome, 207–209
evolution of, 219–220
Ritter, Johann Wilhelm, 36
RNA, 202, 205–207
as enzyme, 219–220
translation and, 207–209
RNA polymerase, 206–207, 208, 209, 236
Rohrer, Heinrich, 95
Russell, Bertrand, 244–245
Rutherford, Ernest, 2
Saint Augustine, 15
Saint Thomas Aquinas, 16
Sakamoto, Takeshi, 182–187
Scanning probe microscopes (SPMs), 94, 95–96
Scanning tunneling microscope (STM), 95–96
Schleiden, Matthias Jakob, 33
Schlichta, Paul, 92n
Scholasticism, 16
Schrödinger, Erwin, 6, 63–66, 116, 214
Schrödinger’s cat, 128
Schwann, Theodor, 33
Science (journal), 236
Scientific revolution, 21
Searson, Peter, 2
Second law of thermodynamics, 76–80
free energy and, 82
Maxwell on, 126
Maxwell’s demon and, 128–129, 131–132
molecular machines and, 127–128
molecular storm and, 144
nanoscale systems and, 134–136
Smoluchowski’s trap door, 129–130
as statistical law, 130
violation of, 128–132
vital force and, 136–137
The Secret (Byrne), 3, 11
The Secret (film), 10n
Self-assembly, 100–115
energy vs. entropy and, 108–110
of micelles, 104–105, 106, 107
of snowflakes, 101–103
Sellers, Jim, 183–184
Shape
of molecular machines, 146
myosin II and cellular, 187
of protein, 113–115
Shelley, Mary Wollstonecraft, 34–35
Shelley, Percy Bysshe, 34
SHRIMP, 175
Signaling pathways, 235–237
Sisyphus, 156–158
Smoluchowski, Marian von, 129–130
on chance and laws of probability, 133
simplified version of Maxwell’s demon, 138
Snowflakes, formation of, 82–83, 101–103
Sodium-potassium pump, 212
Soul, 12–14, 16
Descartes and, 20
La Mettrie’s denial of, 24–25
Spacey, Kevin, 48
SPMs. See Scanning probe microscopes (SPMs) Spudich, Jim, 175–176
Stahl, Georg Ernst, 29
Stars, 85
Statistical mechanics, 3, 60–61, 68–69
molecular motion and, 163
Schrödinger and, 65, 69
Statistics, 53–56
Steam engines, as analogy for life, 25n
Stevenson, John, 28
Stiffness, of molecule-thick water layers, 118–120
STM. See Scanning tunneling microscope (STM)
Stoics, 15, 60
The Strategy of Life (Lenoir), 32n
Subba-Rao, Venkatesh, 101
Supernovae, 85
Surface-to-volume ratio, in nanoscale, 98–99
Sutton, Walther, 61
Swerve, 14
Systems biology, 235–237
Szilard, Leo, 131
Targeted drug delivery, 93–94
Teleomechanism, 32–34
Temperature
free energy and, 80–81
molecular motor speed and, 167–168
motion of kinesin and, 179
self-assembly and, 109
Thales, 13
The Theory of Heat (Maxwell), 126
Theory of probability, 48–50
“There’s Plenty of Room at the Bottom” (Feynman), 91–92, 93
Thermal energy, 70, 73, 74
Thermal noise (thermal motion), 72, 100
cellular activity and, 65
chaos and, 145–146, 168, 205, 226
molecular machines and, 122, 123–124, 174
mutations and, 225–226
Thermodynamic equilibrium, 85
Thermodynamics, 60
biology and, 30
first law of, 73
second law of (see Second law of thermodynamics)
This Is Biology (Mayr), 229
Thompson, Benjamin (Count Rumford), 29, 70
Thompson, D’Arcy Wentworth, role of chance in history of life, 7, 57–58, 60, 224–225
Threonine, 151–152
L-Threonine deaminase, 151–152, 153
Thymine, 201, 202
Tight coupling, 159–162, 166, 167
Timaeus (Plato), 26
Timoféeff, Nikolai, 62, 63, 64
TIMP-2, 233–234
TIRF, 175
Topoisomerase, 203, 204
Tourney, Christopher, 92n
Transactions of the Scientific Society of Göttingen (journal), 62
Transcription, 202, 205–207, 208
Transfer RNA (tRNA), 207–209
Transistor, 122
Transition state, in chemical reactions, 146–147, 148
Translation, 202, 207–209
tRNA synthetases, 208–209
Tropomyosin, 189
Tunneling, 95–96 21 (film), 48
Universe, 243–246
Uracil, 205–206
UTP, 206
The Vengeful Faculty (La Mettrie), 23
Vesalius, Andreas, 19
Vesalius, Basilius, 18
Vesicles, 106, 107, 182
Vibrational energy, ATP/ADP conversion and, 159
Vinci, Leonardo da, 49
Virchow, Rudolf, 33
Virtual cells, 236
Viruses, self-assembly of, 110
Viscosity, 98
Vital forces, 32–33
experiments disproving necessity of, 38–40
explanation of life and, 60
impossibility of perpetuum mobile and, 137
See also Vitalism/vitalists
“Vitalisms and Animalisms” (Monod), 58–59
Vitalism/vitalists, 7, 12–13, 14, 15, 238–239
chance vs. necessity and, 60
conservation of energy and repudiation of, 36–41
discrediting of, 60
epigenesis and, 31–32
Galen and, 17
irritability and, 34–36
teleomechanism and, 32–34
Voltage, across the membrane, 194
Voltaire, 21, 58
Waiting state, 177–178
Walker, John E., 195
Walking transport motors
kinesin-1, 176–181, 232
myosin V, 176, 182–187, 189, 192
Wallace, Alfred Russell, 41
Watch, as analogy for living organism, 214–216
Water molecules
cooperativity and, 117–120
hydrogen bonds and, 110–111
Watson, James, 6, 201–202
Wave mechanics, 63
Weinberg, Steven, 241
Weizman Institute of Science, 219
“What I Believe” (Russell), 244–245
What Is Life? (Schrödinger), 6, 63–64, 225
Xenophanes, 13
X-synthase, 171
Yanagida, Toshio, 167, 179
Young’s modulus, 98
Zeno of Citium, 15
Zimmer, Karl, 62, 63, 64
Hoffmann, Peter M., Life's Ratchet: How Molecular Machines Extract Order from Chaos